Open source parts of Android: missing driver blobs and Google proprietary apps.
Google develops its features in secret, and then releases the source afterwards.
AOSP does contain userland apps besides system stuff: http://arstechnica.com/gadgets/2014/07/exploring-the-world-of-foss-android-can-a-smartphone-be-open-source/, but many are leftovers from the past and not maintained anymore.